MD is a program which simulates the behavior of a collection of N particles in a box, by computing their positions, velocities and accelerations at STEP_NUM regularly spaced times.
The program does some initialization, and then enters an integration loop. The results of each time step are summarized by printing the time, and the kinetic and potential energies (whose sum should be constant).
The main work occurs in the function update; most of the rest of the work is carried out in function compute.
Once you have made a md executable, you need to copy this script file to the same directory that contains the executable, and issue the command qsub md.sh. That submits a request to have the executable program run on 4 processors. You can type showq to see if the request has started yet.
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